Sydney Bristow odkrywa, że jej praca jako agentki SD-6, ściśle tajnego oddziału CIA, skrywa kilka śmiertelnych sekretów, które zagrażają bezpieczeństwu wolnego świata. Mimo ostrzeżeń, Sydney wyjawia swój sekret swojemu narzeczonemu Danny'emu, który później zostaje zamordowany. Sydney odkrywa, że jej ojciec, Jack, również jest SD-6 i że grupa nie jest częścią CIA, ale w rzeczywistości wrogiem Stanów Zjednoczonych. Sydney zwraca się o pomoc do prawdziwego CIA i zostaje zatrudniona jako podwójny agent pod dowództwem oficera operacyjnego Vaughna. Jej misją jest teraz dokończenie swoich spraw w SD-6, jednocześnie zgłaszając swoje ustalenia z powrotem do CIA. Ale kiedy Sydney dowiaduje się, że jej ojciec jest również powiązany z CIA, zaczyna zastanawiać się, gdzie naprawdę leży jego lojalność.

Sydney returns to SD-6 and is assigned with Dixon to travel to Moscow to retrieve some stolen files. But when Sydney discovers that she has inadvertently given SD-6 access to a nuclear weapon, she is forced to travel to Cairo and face a deadly foe. Meanwhile, Will begins to question the circumstances surrounding Danny's death, and Sydney learns of her father's involvement in the murder.

Sydney's life is in mortal danger as she is sent to Madrid to retrieve a 500-year-old sketch that contains a set of numbers and meets up with her deadly nemesis, K-Directorate agent Anna Espinosa. Meanwhile, Will delves deeper into the cause of Danny's death and discovers a very strange anomaly.

Sydney and Dixon go on a dangerous case involving the safety of the United Commerce Organization. Francie confronts Charlie about his secret date with another woman, and Will continues to get closer to the truth about Danny's murder.

Sydney's secret double agent status is jeopardized after she smuggling a biotech engineer into SD-6 from her mission in Berlin. Will meets a woman who confesses that she was having an affair with Danny shortly before his death. Vaughn informs Sydney that her father may be working for a third secret operative agency.

Sydney goes undercover in a mental institution to get information from Shepard, a man who has been unconsciously programmed to be a deadly assassin. Meanwhile, after Sydney becomes convinced that her father was responsible for the death of her mother 20 years earlier. Will discovers the true identity of the woman who claimed having an affair with Danny and Francie is relieved to learn that Charlie is not having an affair other woman. Marshall finds the computer worm planted in the SD-6 mainframe by the CIA.

While helping Shepard escape from the asylum in Bucharest, Sydney discovers the shocking connection he has with her past. Meanwhile, after tracking the computer virus secretly planted by the CIA, Sloane is confronted by Alliance representative Alain Christophe, who suggests that one or more moles may have infiltrated SD-6. Will continues to investigate the woman claiming to be Danny's mistress and Sydney finds out the truth about her father's involvement in her mother's death 20 years earlier.

Sydney must undergo an extensive lie detector test to satisfy Sloane's frantic search for the SD-6 mole. Meanwhile, with nemesis Anna Espinosa following her every move, Sydney seeks out the connection that a device may have to the 500-year-old prophetic Rambaldi sketch. The mystery of Kate Jones deepens as Will continues to investigate Danny's death; and Sydney discovers that a keepsake from her mother Laura contains more disturbing connections into Jack's past alliances.

Sydney's life is placed in mortal danger when Sloane is informed by his superior that she is the SD-6 mole. Meanwhile, Dixon's life hangs in the balance after he is shot on a mission, and Will realizes that his discovery of Kate Jones' pin could uncover some unexpected information.

Sydney briefs her CIA handler, Agent Vaughn, on her recent captivity at SD-6 and is surprised when he unexpectedly gives her a Christmas gift. Meanwhile Jack has to find a way to save Sydney when he discovers that Sloane has ordered her tortured and killed for being the suspected SD-6 mole. Will may be making the mistake of his life when he begins to research a name heard on a mysterious audiocassette -- SD-6.

Sydney is grateful and proud of her father after he saves her life while on a case in Havana. But her admiration is short lived when Vaughn discovers further evidence that Jack may have been responsible for the deaths of over a dozen CIA officers many years earlier.

When armed intruders take over SD-6, led by McKenas Cole, a man bent on exacting revenge on ex-boss Sloane, Sydney and Jack must work together to save their colleagues. Meanwhile, Will fears that his investigation of SD-6 and its link to the murder of Eloise Kurtz is placing his life in jeopardy.

Vaughn disobeys orders and attempts to help Sydney and Jack avert the destruction of SD-6 headquarters and all its occupants. Meanwhile, McKenas Cole continues his vendetta against Sloane and searches for a mysterious device. A desperate but determined woman convince Will to continue his investigation of SD-6 and the imprisonment of David McNeil.

Sydney and Dixon are sent to Las Vegas to gather information from a K-Directorate agent who has ties to the group that attacked and nearly destroyed SD-6. Meanwhile, Sydney learns some shocking news about Francie's fiancé, Charlie, Will begins his journey in discovering what SD-6 really is, and Jack continues to try to be more of a father to Sydney when he helps her decide whether or not to continue with graduate school.

Vaughn asks Sydney to use her friendship with Sloane's wife, Emily, to gain access to a mysterious Rambaldi book which happens to be under lock and key in a safe at Sloane's home. Meanwhile, Will is kidnapped and told to drop his investigation of SD-6 or risk the lives of his family and friends, including Sydney's.

Sydney is tested by the DSR to discover her mysterious link to a chilling 500-year-old picture and prophecy foretold in a Rambaldi manuscript. Meanwhile, after uncovering the identity of the rogue group leader, "The Man," Sloane learns through fellow Alliance of Twelve member Edward Poole that a close friend may be in cahoots with the enemy.

While the FBI detains and questions Sydney about her past and possible ties to a mysterious Rambaldi doomsday prophecy, Vaughn and Jack must race to free her and find a way to clear her name before her cover is blown and SD-6 is made aware of the situation. Once the rescue op has been launched, in her quest to prove her innocence, Sydney shocks even her usually unflappable father when she makes a chilling discovery that may unravel the mystery of the 500-year-old prophecy – she finds proof that Rambaldi's writings may hold more truth about an alleged weapon of mass destruction - and the fate of her own family.

While on a case to track the activities of Khasinau, a.k.a. "The Man," Sydney runs into her ex-lover, Noah Hicks, who broke her heart and left without saying goodbye five years earlier. Meanwhile, Sydney tells Sloane that she wants to find her mother; Jack is ordered to see CIA psychiatrist Dr. Barnett to help him deal with his churning emotions after discovering that his wife may still be alive; and Will and Francie become suspicious of Sydney's activities after finding one of her airline ticket stubs.

In order to catch Khasinau and get closer to finding her mother, Sydney and Vaughn set up an undercover transaction for a Rambaldi artifact with Khasinau's representative, Mr. Sark. But Sydney's cover may be compromised when a SD-6 agent is sent in to thwart the sale. Meanwhile, Will is enticed to continue his investigation of SD-6 when he learns the identity of one of his kidnappers. Emily tells Sydney that she knows about SD-6, which forces Sloane to make the most difficult decision of his life.

Will's life is about to change as he is sent to find the person responsible for leaking information to him about SD-6. Meanwhile, Sloane finds himself on the cusp of finally tracking down Khasinau when SD-6 captures "The Man's" right-hand man, Mr. Sark. Dixon becomes suspicious of Sydney's activities.

In order to save Will's life, Sydney and Vaughn must destroy a familiar looking Rambaldi device, while Jack makes a risky deal with Khasinau's representative, Mr. Sark. Meanwhile, the CIA believes that one of their own is a mole for "The Man"; the Alliance comes to a decision regarding the fate of Emily Sloane; Dixon's suspicions about Sydney intensify; and Sydney finds herself face-to-face with "The Man."